The story was very meh and nothing was really memorable. More free form missions were cool in theory but overpowered AI, buggy stealth and bad parcouring took all the joy out of that. Unity was still quite buggy and unpolished years after release for me (crashes, freezes, 5 fps sometimes, clipping bugs with no end). May not have that fancy lighting engine but at least it works. The side quests in Syndicate are generally better too, there's some fun ones.
It's completely optional IIRC, and I found it "accidentally" and it was a really pleasent surprise. Plus Syndicate has one really really really cool section that I won't spoil. The story in both games is pretty meh but Syndicate at least has some fun characters, whereas I honestly can't remember anyone outside of Arno and Elise in Unity. The music is largely absent in Unity as well, whereas Syndicate has a lot of really fantastic tracks.
Syndicate has full day/night progression and weather progression while Unity is static. Unity may look slightly better but Syndicate is far more dynamic. Syndicate is a fun little mix of classic AC stuff with a few additions and tweaks. With the wider city you get to drive around stage coaches as opposed to running everywhere like in Unity, which I liked. I also have to say that the grappling hook is great, and gives the game a different kind of flow. Syndicate's London is a lot "wider" which acutally makes parkour less frustrating, there's less unintentional grabs/climbs, whatever.
Syndicate's combat is a bit too easy and the mechanic where enemis become staggered and move around like god damn zombies is honestly way too fucking silly even if the finishers that you can pull off thanks to this look amazing. Also Unity's Paris has a nice intricate feel. And the crowds, especially with how they can be part of the gameplay, are cool. It has better combat, and the parkour is "deeper".